Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. - David J. Reiss; Nitin S. Baliga; Richard Bonneau (BMC Bioinform., 2006)

The Gaggle: An open-source software system for integrating bioinformatics software and data sources. - Paul T. Shannon; David J. Reiss; Richard Bonneau; Nitin S. Baliga (BMC Bioinform., 2006)

BioNetBuilder: automatic integration of biological networks. - Iliana Avila-Campillo; Kevin Drew; John Lin; David J. Reiss; Richard Bonneau (Bioinform., 2007)

Modeling gene regulation and spatial organization of sequence based motifs. - Jochen Supper; Claas aufm Kampe; Dierk Wanke; Kenneth W. Berendzen; Klaus Harter; Richard Bonneau; Andreas Zell (BIBE, 2008)

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters. - Thadeous Kacmarczyk; Peter Waltman; Ashley Bate; Patrick Eichenberger; Richard Bonneau (PLoS Comput. Biol., 2011)

Session introduction. - Jason E. McDermott; Pascal Braun; Richard Bonneau; Daniel R. Hyduke (Pacific Symposium on Biocomputing, 2012)

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. - Alex Greenfield; Christoph Hafemeister; Richard Bonneau (Bioinform., 2013)

Parametric Bayesian priors and better choice of negative examples improve protein function prediction. - Noah Youngs; Duncan Penfold-Brown; Kevin Drew; Dennis E. Shasha; Richard Bonneau (Bioinform., 2013)

Negative Example Selection for Protein Function Prediction: The NoGO Database. - Noah Youngs; Duncan Penfold-Brown; Richard Bonneau; Dennis E. Shasha (PLoS Comput. Biol., 2014)

Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. - Bowen Yu 004; Harish Doraiswamy; Xi Chen; Emily R. Miraldi; Mario Luis Arrieta-Ortiz; Christoph Hafemeister; Aviv Madar; Richard Bonneau; Cláudio T. Silva (IEEE Trans. Vis. Comput. Graph., 2014)

Positive-Unlabeled Learning in the Face of Labeling Bias. - Noah Youngs; Dennis E. Shasha; Richard Bonneau (ICDM Workshops, 2015)

Inter-species pathway perturbation prediction via data-driven detection of functional homology. - Christoph Hafemeister; Roberto Romero; Erhan Bilal; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Richard Bonneau; Adi L. Tarca (Bioinform., 2015)

Political Expression and Action on Social Media: Exploring the Relationship Between Lower- and Higher-Threshold Political Activities Among Twitter Users in Italy. - Cristian Vaccari; Augusto Valeriani; Pablo Barberá; Richard Bonneau; John T. Jost; Jonathan Nagler; Joshua A. Tucker (J. Comput. Mediat. Commun., 2015)

Sparse and Compositionally Robust Inference of Microbial Ecological Networks. - Zachary D. Kurtz; Christian L. Müller; Emily R. Miraldi; Dan R. Littman; Martin J. Blaser; Richard A. Bonneau (PLoS Comput. Biol., 2015)

Big Data, Social Media, and Protest: Foundations for a Research Agenda. - Joshua A. Tucker; Jonathan Nagler; Megan Macduffee Metzger; Pablo Barberá; Duncan Penfold-Brown; Richard Bonneau (Computational Social Science, 2016)

Text Classification for Automatic Detection of E-Cigarette Use and Use for Smoking Cessation from Twitter: A Feasibility Pilot. - Yin Aphinyanaphongs; Armine Lulejian; Duncan Penfold-Brown; Richard Bonneau; Paul Krebs (PSB, 2016)

Accurate de novo design of hyperstable constrained peptides. - Gaurav Bhardwaj; Vikram Khipple Mulligan; Christopher D. Bahl; Jason M. Gilmore; Peta J. Harvey; Olivier Cheneval; Garry W. Buchko; Surya V. S. R. K. Pulavarti; Quentin Kaas; Alexander Eletsky; Po-Ssu Huang; William A. Johnsen; et al. (Nat., 2016)

Fused Regression for Multi-source Gene Regulatory Network Inference. - Kari Y. Lam; Zachary M. Westrick; Christian L. Müller; Lionel A. Christiaen; Richard Bonneau (PLoS Comput. Biol., 2016)

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. - Ramya Raviram; Pedro P. Rocha; Christian L. Müller; Emily R. Miraldi; Sana Badri; Yi Fu; Emily Swanzey; Charlotte Proudhon; Valentina Snetkova; Richard Bonneau; Jane A. Skok (PLoS Comput. Biol., 2016)

Detecting Bots on Russian Political Twitter. - Denis Stukal; Sergey Sanovich; Richard Bonneau; Joshua A. Tucker (Big Data, 2017)

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. - Julia Koehler Leman; Sergey Lyskov; Richard Bonneau (BMC Bioinform., 2017)

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. - Kevin Drew; Christian L. Müller; Richard Bonneau; Edward M. Marcotte (PLoS Comput. Biol., 2017)

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. - Tarmo Äijö; Christian L. Müller; Richard Bonneau (Bioinform., 2018)

deepNF: deep network fusion for protein function prediction. - Vladimir Gligorijevic; Meet Barot; Richard Bonneau (Bioinform., 2018)

Towards region-specific propagation of protein functions. - Da Chen Emily Koo; Richard Bonneau (Bioinform., 2019)

Multi-study inference of regulatory networks for more accurate models of gene regulation. - Dayanne M. Castro; Nicholas R. de Veaux; Emily R. Miraldi; Richard Bonneau (PLoS Comput. Biol., 2019)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

An Automatic Framework to Continuously Monitor Multi-Platform Information Spread. - Zhouhan Chen; Kevin Aslett; Jen Rosiere Reynolds; Juliana Freire; Jonathan Nagler; Joshua A. Tucker; Richard Bonneau (MISINFO@WWW, 2021)

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. - Meet Barot; Vladimir Gligorijevic; Kyunghyun Cho; Richard Bonneau (Bioinform., 2021)

YouTube Recommendations and Effects on Sharing Across Online Social Platforms. - Cody Buntain; Richard Bonneau; Jonathan Nagler; Joshua A. Tucker (Proc. ACM Hum. Comput. Interact., 2021)

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. - Matthew R. Dillon; Evan Bolyen; Anja Adamov; Aeriel Belk; Emily Borsom; Zachary Burcham; Justine W. Debelius; Heather Deel; Alex Emmons; Mehrbod Estaki; Chloe Herman; Christopher R. Keefe; et al. (PLoS Comput. Biol., 2021)

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. - Andreas Tjärnberg; Omar Mahmood; Christopher A. Jackson; Giuseppe-Antonio Saldi; Kyunghyun Cho; Lionel A. Christiaen; Richard A. Bonneau (PLoS Comput. Biol., 2021)

A convolutional neural network for common coordinate registration of high-resolution histology images. - Aidan C. Daly; Krzysztof J. Geras; Richard Bonneau (Bioinform., 2021)

Dictionary-Assisted Supervised Contrastive Learning. - Patrick Y. Wu; Richard Bonneau; Joshua A. Tucker; Jonathan Nagler (EMNLP, 2022)

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. - Claudia Skok Gibbs; Christopher A. Jackson; Giuseppe-Antonio Saldi; Andreas Tjärnberg; Aashna Shah; Aaron Watters; Nicholas De Veaux; Konstantine Tchourine; Ren Yi; Tymor Hamamsy; Dayanne M. Castro; Nicholas Carriero; et al. (Bioinform., 2022)

Multi-segment preserving sampling for deep manifold sampler. - Daniel Berenberg; Jae Hyeon Lee; Simon Kelow; Ji Won Park; Andrew M. Watkins; Vladimir Gligorijevic; Richard Bonneau; Stephen Ra; Kyunghyun Cho (CoRR, 2022)

PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design. - Ji Won Park; Samuel Stanton; Saeed Saremi; Andrew M. Watkins; Henri Dwyer; Vladimir Gligorijevic; Richard Bonneau; Stephen Ra; Kyunghyun Cho (CoRR, 2022)

A Pareto-optimal compositional energy-based model for sampling and optimization of protein sequences. - Natasa Tagasovska; Nathan C. Frey; Andreas Loukas; Isidro Hötzel; Julien Lafrance-Vanasse; Ryan Lewis Kelly; Yan Wu 027; Arvind Rajpal; Richard Bonneau; Kyunghyun Cho; Stephen Ra; Vladimir Gligorijevic (CoRR, 2022)

NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. - Ren Yi; Kyunghyun Cho; Richard Bonneau (Bioinform., 2022)

Measuring the Ideology of Audiences for Web Links and Domains Using Differentially Private Engagement Data. - Cody Buntain; Richard Bonneau; Jonathan Nagler; Joshua A. Tucker (ICWSM, 2023)

OpenProteinSet: Training data for structural biology at scale. - Gustaf Ahdritz; Nazim Bouatta; Sachin Kadyan; Lukas Jarosch; Daniel Berenberg; Ian Fisk; Andrew M. Watkins; Stephen Ra; Richard Bonneau; Mohammed AlQuraishi (NeurIPS, 2023)

AbDiffuser: full-atom generation of in-vitro functioning antibodies. - Karolis Martinkus; Jan Ludwiczak; Wei-Ching Liang; Julien Lafrance-Vanasse; Isidro Hötzel; Arvind Rajpal; Yan Wu 027; Kyunghyun Cho; Richard Bonneau; Vladimir Gligorijevic; Andreas Loukas (NeurIPS, 2023)

TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. - Emmi Jokinen; Alexandru Dumitrescu; Jani Huuhtanen; Vladimir Gligorijevic; Satu Mustjoki; Richard Bonneau; Markus Heinonen; Harri Lähdesmäki (Bioinform., 2023)

Protein Discovery with Discrete Walk-Jump Sampling. - Nathan C. Frey; Daniel Berenberg; Karina Zadorozhny; Joseph Kleinhenz; Julien Lafrance-Vanasse; Isidro Hötzel; Yan Wu 027; Stephen Ra; Richard Bonneau; Kyunghyun Cho; Andreas Loukas; Vladimir Gligorijevic; et al. (ICLR, 2024)

LLMs are Highly-Constrained Biophysical Sequence Optimizers. - Angelica Chen; Samuel Don Stanton; Robert G. Alberstein; Andrew M. Watkins; Richard Bonneau; Vladimir Gligorijevic; Kyunghyun Cho; Nathan C. Frey (CoRR, 2024)

Tokenized and continuous embedding compressions of protein sequence and structure. - Amy X. Lu; Wilson Yan; Kevin K. Yang; Vladimir Gligorijevic; Kyunghyun Cho; Pieter Abbeel; Richard Bonneau; Nathan C. Frey (Patterns, 2025)

Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins. - Frédéric A. Dreyer; Jan Ludwiczak; Karolis Martinkus; Brennan Abanades; Robert G. Alberstein; Pan Kessel; Pranav Rao; Jae Hyeon Lee; Richard Bonneau; Andrew M. Watkins; Franziska Seeger (CoRR, 2025)